Expansions of CAG repeats in specific human genes cause numerous neurological diseases, including Huntington disease, myotonic dystrophy, and several spinocerebellar ataxias. These diseases cause immense human suffering, with few potential treatments, and no cures. Our long-term goal is to determine the basis for CAG repeat instability in human patients. Our approach is to combine the strengths of a novel selection assay in human cells with the power of mouse models to discover processes that are responsible for repeat instability in human disease. This application focuses on the role of transcription in triggering CAG repeat instability. Our overarching hypothesis is that transcription promotes formation of repeat-dependent secondary structures that call into play various repair proteins whose actions change the length of the repeat tract. Using siRNA knockdowns and chemical treatments in human cells, we showed that transcription-induced repeat instability was either enhanced or suppressed by several processes, including mismatch repair, transcription-coupled nucleotide excision repair (NER), single-strand break (SSB) repair, double-strand break (DSB) repair, proteasome degradation, transcriptional R-loops, antisense transcription, and DNA damage signaling pathways. In every single case, the effect of the interfering agent was manifest only when there was active transcription through the repeat tract. Critically, we showed that eliminating nucleotide excision repair in a SCA1 mouse model virtually eliminated CAG instability in striatum, in accord with results in human cells. In this application, we propose to concentrate on three striking aspects of our current work. In Aim 1, we propose to investigate in human cells and mice our observation that convergent transcription through a CAG tract-simultaneous sense and antisense transcription-not only synergistically increases repeat instability, but also triggers apoptosis, providing a potential link to disease pathogenesis. In Aim 2, we propose to test the inference that transcription drives repeat instability via NER and SSB repair in vitro, in cells, and in mice. In Aim 3, we propose to exploit the CAG-specific zinc-finger nucleases we developed in the current grant period to investigate the roles of DSBs and strand-specific SSBs in CAG repeat instability in human cells and mouse models. Our overall goal is to delineate those processes that are responsible for both germline and somatic CAG repeat instability that characterizes several neurological diseases.